| Class | Description |
|---|---|
| AlignmentEditor |
Implementation of methods and data structures for GUIAlignmentEditor.
|
| AlignmentOperations |
Class to handle any kinds of alignment operations.
|
| CodemlOptions |
Support class for the GUICodemlOptions for choosing (other) Codeml options.
|
| CodemlTask |
Implementation of a background task for Codeml execution.
|
| CodemlTP |
Class to handle PAML (Codeml) results and input data.
|
| CSVTableModel |
Implementation of specific Table Model for Comma Separated Values files.
|
| DatamonkeyTP |
Class to handle Datamonkey results and generate data from models SLAC, FEL, REL, MEME and FUBAR.
|
| FileFormat |
Class for storing basic information about Sequence Files.
|
| FileFormatConverter |
Implementation of functions to read/write several formats of MSA files.
|
| FileFormatReader |
Class to handle the reading/writing of non-aligned sequences files.
|
| GenericJarTask |
Implementation of background task to run any java (jar) program file.
Used for java based programs. |
| GnuplotTask |
Implementation of a background task for Gnuplot execution.
|
| GUI |
IMPACT_S main class/window.
|
| GUIAboutBox |
GUI About Box.
|
| GUIAlignmentEditor |
Implementation of MSA Editor / Viewer, also topology (re)estimation through PhyML.
|
| GUIAlignmentFiltering |
Implementation of alignment filtering operation.
|
| GUICodemlOptions |
GUI implementing Codeml options for the user.
|
| GUIColorSchemes |
Class to permit visual understanding of scheme colors (working like in a legend) and
to allow color selection in the selected scheme.
|
| GUIDialogs |
Implementation of several dialog messages.
|
| GUIFileChooser |
Implementation of a File Chooser.
|
| GUIFileFormatConverter |
Implementation of MSA File Format Converter.
Supports conversion between formats like Mase, Fasta, Clustal and Phylip |
| GUIGnuplotOptions |
Class to allow the creation / visualization of graphs for
TreeSAAP Sliding Window properties files.
|
| GUIINFO |
Specific GUI informative window.
|
| GUIInitBox |
A simple initialization box.
|
| GUIPDBColorSeq |
GUI to allow user to color/exhibit the PDB file amino-acid sequence.
|
| GUIPDBTool |
Download PDB and FASTA files from RCSB, or
PDB files having only one chain, from Swiss Model - Template Library.
|
| GUIPhyMLOptions |
Implementation of PhyML Options selection.
|
| GUIPreferences |
GUI for user preferences.
|
| GUIProgExecOutput |
Implementation of external program execution output viewer.
|
| GUIProtToSwissModel |
GUI to allow submission of data to Swiss Model and obtain modelled PDB.
|
| GUIResultsView |
Implementation of Comma Separated Values (CSV) format files viewer.
|
| MSAColumnColorRenderer |
Implementation of specific Table Cell Renderer for presenting selected columns in MSA table.
|
| MSATableModel |
Implementation of specific Table Model for Multiple Sequence Alignments.
|
| PDBSeqColClrRenderer |
Implementation of specific Table Cell Renderer for presenting selected colors in PDB sequence table.
|
| PDBSeqTableModel |
Implementation of specific Table Model for PDB Sequence Coloring.
|
| PhyMLTask |
Implementation of a background task for PhyML execution.
|
| ProtToSwissModel |
Class to handle Swiss-Model submission and modeled pdb retrieval.
|
| RCSBTools |
Basic functionality for downloading PDB files from RCSB website.
|
| ResultsN3DTP |
Class to handle necessary computation and data storage for general or final results.
Results from previous tabs and from resources like Jmol and Swiss Model. |
| ResultsView |
Implementation of several methods to allow reading Comma Separated Values (CSV) files.
|
| SequenceTranslator |
Translate sequences from DNA or RNA into Protein,
allowing choice of a specific translation table and start site.
|
| Statistics |
Class implementing some distributions, tests, etc.
|
| TreeSAAPTP |
Class for handling TreeSAAP results and input data.
|
| Utilities |
Utilities used across the whole software package.
|